Related papers: Force Feedback Effects on Single Molecule Hopping …
The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds…
We deduce a fully analytical model to predict the artifacts of the measuring device handles in Single Molecule Force Spectroscopy experiments. As we show, neglecting the effects of the handle stiffness can lead to crucial overestimation or…
One-dimensional hopping model is useful to describe the motion of microscopic particle in thermal noise environment, such as motor proteins. Recent experiments about the new generation of light-driven rotary molecular motors found that, the…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
We investigate the possibility of extending the notion of temperature in a stochastic model for the RNA/protein folding driven out of equilibrium. We simulate the dynamics of a small RNA hairpin subject to an external pulling force, which…
Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
In cellular environment, confinement and macromulecular crowding play an important role on thermal stability and folding kinetics of a protein. We have resorted to a generalized version of the Wako-Saito-Munoz-Eaton model for protein…
This work proposes an investigation of the fracturing behavior of polymer nanocomposites. Towards this end, the study leverages the analysis of a large bulk of fracture tests from the literature with the goal of critically investigating the…
We investigated frictional effects on the folding rates of a human telomerase hairpin (hTR HP) and H-type pseudoknot from the Beet Western Yellow Virus (BWYV PK) using simulations of the Three Interaction Site (TIS) model for RNA. The heat…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
We present an extremely simplified model of multiple-domains polymer stretching in an atomic force microscopy experiment. We portray each module as a binary set of contacts and decompose the system energy into a harmonic term (the…
Quantum kinetically constrained models can exhibit a wealth of dynamical phenomena ranging from anomalous transport to Hilbert-space fragmentation (HSF). We study a class of one-dimensional particle number conserving systems where particle…
In our original article (Phys. Chem. Chem. Phys., 2012, 14, 60446053) a convergence problem resulted in an averaging error in computing the entropy from a set of Wang-Landau Monte-Carlo simulations. Here we report corrected results for the…
We solve a two dimensional model for polymer chain folding in the presence of mechanical pulling force ($f$) exactly using equilibrium statistical mechanics. Using analytically derived expression for the partition function we determine the…
External biasing forces are often applied to enhance sampling in regions of phase space which would otherwise be rarely observed. While the typical goal of these experiments is to calculate the potential of mean force (PMF) along the…
Kinetics of folding of a protein held in a force-clamp are compared to an unconstrained folding. The comparison is made within a simple topology-based dynamical model of ubiquitin. We demonstrate that the experimentally observed variations…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Relevant information about the nature of the dynamics of ions in electrolytes can be obtained by studying the nonlinear dependence on an applied electric field. Here we use molecular dynamics (MD) simulations to study the field effects for…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…